Trajectory SP912

Force field: martini_v2.2
Simulation length (ns): 5000
Electric field (kJ mol-1 nm-1 e-1): 0
Temperature (K): 300 (v-rescale)
Pressure (bar): 1 (Parrinello-rahman semiisotropic)
Number of particles: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P246 NC03982
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
NTRGSWSNKRLSPR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 4
  Polar: 6
Electrostatic Dipolar Moment (e nm): 2.63
Longitudinal (e nm): 2.21
Transversal (e nm): 1.43
Hydrophobic Dipolar Moment (nm): 0.52
Longitudinal (nm): 0.48
Transversal (nm): 0.2
Secondary structure: Helix
Activity:

Download Files
  ITP file.
  JSON file.
  PDB file.

Click on any component to highlight it from the plot.
Upper leaflet
Lower leaflet

Lipids


Membrane model for: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

Molecular Dynamics based descriptors
Average and standard deviation, calculated using the autocorrelation function (for time series) or the width of the distribution, for the last microsecond of the trajectory

Area per lipid
Membrane (nm2): 0.6421490 ± 0.0011029
Upper leaflet (nm2): 0.6421490 ± 0.0011029
Lower leaflet (nm2): 0.6421490 ± 0.0011029
Average Z coordinate
Peptide (nm): 4.7484800 ± 0.0332258
First Residue (nm): 4.6763900 ± 0.0461242
Last Residue (nm): 4.6855400 ± 0.0527707
Membrane (nm): 6.840900 ± 0.011542
Upper leaflet Head Group (nm): 8.8023700 ± 0.0138304
Lower leaflet Head Group (nm): 4.87865000 ± 0.00923998
Bilayer Thickness (nm): 3.923730 ± 0.016633
Peptide insertion (nm): 0.1301680 ± 0.0344867
Contacts
Peptide - Water: 28.612500 ± 0.822384
Peptide - Head groups: 11.20750 ± 0.24908
Peptide - Tail groups: 6.730000 ± 0.274945
Tilt (°): 88.9471 ± 2.1961
PepDF:
5(ns):  CVS
Displacement (nm): 0.7312440 ± 0.0305764
Precession(°): 0.200967 ± 2.347300
50(ns)  CVS
Displacement (nm): 2.0363900 ± 0.0902529
Precession(°): -1.59731 ± 6.81888
100(ns)  CVS
Displacement(nm): 2.56757 ± 0.15285
Precession(°): -4.77455 ± 10.06770
200(ns)  CVS
Displacement(nm): 3.145210 ± 0.214405
Precession(°): -6.48306 ± 13.58250

  Download JSON File.

Peptide Analyses

Peptide Displacement Fingerprint (PepDF)
Lateral displacement vs Rotational Displacement along the trajectory, for different time windows .

Density maps:
2D-density maps of lipids around the peptide along XY and YZ axis, calculated for each lipid type along the last microsecond.

Lipid-Peptide Analyses:

z-Position
Z-coordinate, averaged for differetn parts of the the system: peptide, membrane, first and last backbone (BB) residues and upper of lower leaflet lipids’ headgroups (HGs).
Minimum distance
Minimum distance (nm) between the peptide backbone and the lipids (headgroups and tailgroups).
Number of contacts
Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm.
Lateral density
Lateral density for the different components of the system: headgroups, tail groups, peptide and water.